rs2027471

Variant names:

• chr1-159719598-T-A
• rs2027471
• ENST00000751816.1:n.108-6929T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159719598-T-A
• chr1-159719598-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751816.1(ENSG00000297913):​n.108-6929T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,092 control chromosomes in the GnomAD database, including 8,586 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8586 hom., cov: 33)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 17 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-6929T>A		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-6929T>A		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-6929T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49294 AN: 151974 Hom.: 8578 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.344

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.324 AC: 49321 AN: 152092 Hom.: 8586 Cov.: 33 AF XY: 0.328 AC XY: 24417 AN XY: 74348

African (AFR) AF: 0.214 AC: 8893 AN: 41492

American (AMR) AF: 0.394 AC: 6022 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3133 AN: 5174

South Asian (SAS) AF: 0.319 AC: 1539 AN: 4824

European-Finnish (FIN) AF: 0.381 AC: 4030 AN: 10564

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23265 AN: 67968

Other (OTH) AF: 0.343 AC: 724 AN: 2108

Alfa AF: 0.332 Hom.: 1126

Bravo AF: 0.321

Asia WGS AF: 0.451 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.82
PhyloP100		-0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2027471;

hg19: chr1-159689388;

COSMIC: COSV107159922;